diff options
Diffstat (limited to 'CakeModel.R')
| -rw-r--r-- | CakeModel.R | 42 |
1 files changed, 24 insertions, 18 deletions
diff --git a/CakeModel.R b/CakeModel.R index 3a32779..116ef6b 100644 --- a/CakeModel.R +++ b/CakeModel.R @@ -4,8 +4,8 @@ # Portions Johannes Ranke, 2010 # Contact: mkin-devel@lists.berlios.de -# Modifications developed by Tessella for Syngenta: Copyright (C) 2011-2016 Syngenta -# Tessella Project Reference: 6245, 7247, 8361, 7414 +# Modifications developed by Tessella for Syngenta: Copyright (C) 2011-2020 Syngenta +# Tessella Project Reference: 6245, 7247, 8361, 7414, 10091 # The CAKE R modules are free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -22,6 +22,8 @@ CakeModel <- function(..., use_of_ff = "max") { + # While spec is modified throughout this function, topology is added as-is to the returned model + topology <- list(...) spec <- list(...) obs_vars <- names(spec) @@ -33,7 +35,7 @@ CakeModel <- function(..., use_of_ff = "max") parms <- vector() diffs <- vector() map <- list() - nlt = list() + nlt <- list() # Establish list of differential equations for (varname in obs_vars) @@ -74,7 +76,7 @@ CakeModel <- function(..., use_of_ff = "max") ff <- vector() decline_term <- paste(nonlinear_term, "*", new_boxes[[1]]) } else { # otherwise no decline term needed here - decline_term = "0" + decline_term <- "0" } } else { k_term <- paste("k", new_boxes[[1]], sep="_") @@ -102,9 +104,9 @@ CakeModel <- function(..., use_of_ff = "max") # Construct and add DFOP term and add DFOP parameters if needed if(spec[[varname]]$type == "DFOP") { - k1_term = paste("k1", varname, sep="_") - k2_term = paste("k2", varname, sep="_") - g_term = paste("g", varname, sep="_") + k1_term <- paste("k1", varname, sep="_") + k2_term <- paste("k2", varname, sep="_") + g_term <- paste("g", varname, sep="_") new_parms <- c(k1_term, k2_term, g_term) ff <- vector() @@ -121,7 +123,8 @@ CakeModel <- function(..., use_of_ff = "max") first_nonlinear_term <- paste(k1_term, new_boxes[[1]], sep=" * ") second_nonlinear_term <- paste(k2_term, new_boxes[[2]], sep=" * ") - overall_term_for_formation <- paste("(", g_term, " * ", first_nonlinear_term, " + (1 - ", g_term, ") *", second_nonlinear_term, ")") + # CU-150: formation has already been accounted for on the formation into the two sub-compartments; it does not need to be factored in again on the way out + overall_term_for_formation <- paste("(", first_nonlinear_term, " + ", second_nonlinear_term, ")") spec[[varname]]$nlt <- overall_term_for_formation new_diffs[[1]] <- paste(new_diffs[[1]], "-", first_nonlinear_term) @@ -177,23 +180,23 @@ CakeModel <- function(..., use_of_ff = "max") # There is only one output, so no need for any flow fractions. Just add the whole flow from the parent formation_term <- spec[[varname]]$nlt } else { - fraction_to_target = paste("f", varname, "to", target, sep="_") - fraction_not_to_target = paste("(1 - ", fraction_to_target, ")", sep="") + fraction_to_target <- paste("f", varname, "to", target, sep="_") + fraction_not_to_target <- paste("(1 - ", fraction_to_target, ")", sep="") if(is.null(fraction_left)) { - fraction_really_to_target = fraction_to_target - fraction_left = fraction_not_to_target + fraction_really_to_target <- fraction_to_target + fraction_left <- fraction_not_to_target } else { # If this is the last output and there is no sink, it gets what's left if ( target==tail(to,1) && !spec[[varname]]$sink ) { - fraction_really_to_target = fraction_left + fraction_really_to_target <- fraction_left } else { - fraction_really_to_target = fraction_to_target - fraction_left = paste(fraction_left, " - ", fraction_to_target, sep="") + fraction_really_to_target <- fraction_to_target + fraction_left <- paste(fraction_left, " - ", fraction_to_target, sep="") } } - ff[target] = fraction_really_to_target + ff[target] <- fraction_really_to_target formation_term <- paste(ff[target], "*", spec[[varname]]$nlt) # Add the flow fraction parameter (if it exists) @@ -218,9 +221,12 @@ CakeModel <- function(..., use_of_ff = "max") } } - model <- list(diffs = diffs, parms = parms, map = map, use_of_ff = use_of_ff) + model <- list(diffs = diffs, parms = parms, map = map, use_of_ff = use_of_ff, topology = topology) - if (exists("ff")) model$ff = ff + if (exists("ff")) { + model$ff <- ff + } + class(model) <- "mkinmod" invisible(model) } |